Atomistry » Calcium » PDB 5egt-5eyg » 5ele
Atomistry »
  Calcium »
    PDB 5egt-5eyg »
      5ele »

Calcium in PDB 5ele: Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y

Protein crystallography data

The structure of Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y, PDB code: 5ele was solved by J.E.Heggelund, D.Burschowsky, U.Krengel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.14 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.543, 82.973, 196.555, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 22.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y (pdb code 5ele). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y, PDB code: 5ele:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 5ele

Go back to Calcium Binding Sites List in 5ele
Calcium binding site 1 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:14.5
occ:1.00
 O6 A:BCN205 1.9 29.6 1.0
O4 A:BCN205 2.3 22.8 1.0
O22 A:BCN205 2.3 16.7 1.0
OE1 A:GLU79 2.4 16.2 1.0
OE2 F:GLU79 2.4 17.5 1.0
O A:HOH302 2.4 25.6 1.0
OE2 A:GLU79 2.6 16.3 1.0
CD A:GLU79 2.8 17.5 1.0
C6 A:BCN205 3.0 27.7 1.0
N1 A:BCN205 3.1 22.3 1.0
C2 A:BCN205 3.2 18.8 1.0
C4 A:BCN205 3.2 22.2 1.0
C3 A:BCN205 3.2 23.3 1.0
C1 A:BCN205 3.4 20.8 1.0
C5 A:BCN205 3.5 23.4 1.0
CD F:GLU79 3.5 16.6 1.0
CA A:CA204 3.9 14.8 1.0
O F:HOH302 4.1 22.7 1.0
CG F:GLU79 4.2 15.8 1.0
O A:HOH309 4.3 34.2 1.0
CG A:GLU79 4.3 15.9 1.0
O A:HOH346 4.4 53.8 1.0
NZ A:LYS23 4.4 22.3 0.5
O21 A:BCN205 4.4 17.5 1.0
OD1 J:ASN103 4.5 43.9 1.0
OE1 F:GLU79 4.5 16.5 1.0
O A:HOH306 4.5 31.8 1.0
O6 A:BCN203 4.6 23.3 1.0
CB J:ASN103 4.9 37.8 1.0
O J:ASN103 4.9 38.7 1.0
NZ F:LYS23 5.0 35.0 1.0

Calcium binding site 2 out of 10 in 5ele

Go back to Calcium Binding Sites List in 5ele
Calcium binding site 2 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:14.8
occ:1.00
 O6 A:BCN203 2.2 23.3 1.0
O F:HOH302 2.3 22.7 1.0
OE2 A:GLU79 2.3 16.3 1.0
O4 A:BCN203 2.4 24.5 1.0
O21 A:BCN203 2.4 18.6 1.0
OE1 F:GLU79 2.5 16.5 1.0
OE2 F:GLU79 2.5 17.5 1.0
CD F:GLU79 2.8 16.6 1.0
C3 A:BCN203 3.2 26.4 1.0
N1 A:BCN203 3.2 25.1 1.0
C4 A:BCN203 3.3 24.6 1.0
C6 A:BCN203 3.3 25.2 1.0
C2 A:BCN203 3.3 21.7 1.0
CD A:GLU79 3.4 17.5 1.0
C1 A:BCN203 3.6 23.4 1.0
C5 A:BCN203 3.6 24.7 1.0
CA A:CA201 3.9 14.5 1.0
O A:HOH302 4.0 25.6 1.0
CG A:GLU79 4.2 15.9 1.0
O6 A:BCN205 4.2 29.6 1.0
NZ F:LYS23 4.2 35.0 1.0
O A:HOH309 4.3 34.2 1.0
O F:HOH318 4.3 36.9 1.0
ND2 E:ASN103 4.3 40.3 1.0
OE1 A:GLU79 4.4 16.2 1.0
CG F:GLU79 4.4 15.8 1.0
O22 A:BCN203 4.5 18.0 1.0
CB E:ASN103 4.8 38.8 1.0

Calcium binding site 3 out of 10 in 5ele

Go back to Calcium Binding Sites List in 5ele
Calcium binding site 3 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:15.8
occ:1.00
 O6 B:BCN203 2.1 33.9 1.0
O22 B:BCN203 2.3 20.0 1.0
OE2 J:GLU79 2.4 18.5 1.0
O B:HOH303 2.4 27.1 1.0
OE1 B:GLU79 2.4 17.0 1.0
O4 B:BCN203 2.5 27.6 1.0
OE2 B:GLU79 2.5 17.7 1.0
CD B:GLU79 2.9 17.9 1.0
C6 B:BCN203 3.0 31.5 1.0
N1 B:BCN203 3.2 25.8 1.0
C2 B:BCN203 3.2 21.9 1.0
C4 B:BCN203 3.3 26.2 1.0
C3 B:BCN203 3.3 26.4 1.0
C1 B:BCN203 3.5 23.7 1.0
C5 B:BCN203 3.5 27.9 1.0
CD J:GLU79 3.5 16.6 1.0
CA B:CA204 3.9 13.9 1.0
O A:HOH334 4.2 25.9 1.0
CG J:GLU79 4.2 15.3 1.0
O B:HOH304 4.3 38.4 1.0
CG B:GLU79 4.4 14.9 1.0
O6 B:BCN201 4.4 24.0 1.0
O21 B:BCN203 4.4 21.5 1.0
NZ B:LYS23 4.4 26.6 0.5
ND2 I:ASN103 4.4 40.5 1.0
OE1 J:GLU79 4.5 18.1 1.0
O B:HOH354 4.5 35.3 1.0
O J:HOH302 4.6 31.6 1.0
CB I:ASN103 4.9 38.2 1.0

Calcium binding site 4 out of 10 in 5ele

Go back to Calcium Binding Sites List in 5ele
Calcium binding site 4 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca204

b:13.9
occ:1.00
 O6 B:BCN201 2.3 24.0 1.0
OE2 B:GLU79 2.3 17.7 1.0
O21 B:BCN201 2.4 19.3 1.0
O A:HOH334 2.4 25.9 1.0
OE1 J:GLU79 2.5 18.1 1.0
O4 B:BCN201 2.5 22.9 1.0
OE2 J:GLU79 2.5 18.5 1.0
CD J:GLU79 2.9 16.6 1.0
C6 B:BCN201 3.0 25.0 1.0
N1 B:BCN201 3.1 24.5 1.0
C2 B:BCN201 3.2 22.8 1.0
C3 B:BCN201 3.3 23.8 1.0
C4 B:BCN201 3.3 24.5 1.0
C5 B:BCN201 3.4 23.3 1.0
CD B:GLU79 3.5 17.9 1.0
C1 B:BCN201 3.5 24.9 1.0
CA B:CA202 3.9 15.8 1.0
O B:HOH303 4.0 27.1 1.0
CG B:GLU79 4.2 14.9 1.0
O J:HOH307 4.2 28.4 0.6
O B:HOH304 4.3 38.4 1.0
CG J:GLU79 4.4 15.3 1.0
O22 B:BCN201 4.4 21.9 1.0
OE1 B:GLU79 4.4 17.0 1.0
O B:HOH308 4.6 35.7 1.0
O6 B:BCN203 4.7 33.9 1.0
ND2 A:ASN103 4.7 44.8 1.0
O A:ASN103 4.9 42.6 1.0
CB A:ASN103 4.9 38.8 1.0

Calcium binding site 5 out of 10 in 5ele

Go back to Calcium Binding Sites List in 5ele
Calcium binding site 5 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca202

b:15.5
occ:1.00
 O4 C:BCN203 2.2 25.4 1.0
O C:HOH301 2.3 24.6 1.0
O6 C:BCN203 2.3 21.9 1.0
O22 C:BCN203 2.3 16.5 1.0
OE2 I:GLU79 2.3 17.8 1.0
OE1 C:GLU79 2.5 20.4 1.0
OE2 C:GLU79 2.6 21.6 1.0
N1 C:BCN203 2.8 23.1 1.0
CD C:GLU79 2.9 20.6 1.0
C4 C:BCN203 3.2 25.6 1.0
C2 C:BCN203 3.3 20.6 1.0
C6 C:BCN203 3.3 20.6 1.0
C5 C:BCN203 3.4 21.1 1.0
CD I:GLU79 3.5 18.8 1.0
C1 C:BCN203 3.5 20.7 1.0
C3 C:BCN203 3.6 23.5 1.0
NZ C:LYS23 3.7 26.8 0.5
CA C:CA204 4.0 15.2 1.0
O C:HOH361 4.0 27.4 1.0
CG I:GLU79 4.2 17.0 1.0
NZ I:LYS23 4.3 21.2 0.5
CG C:GLU79 4.4 18.8 1.0
O21 C:BCN203 4.4 18.4 1.0
O4 C:BCN201 4.4 22.7 1.0
OE1 I:GLU79 4.5 18.9 1.0
OD1 H:ASN103 4.6 39.7 1.0
O I:HOH302 4.6 17.2 0.5
O H:ASN103 4.9 38.7 1.0
CB H:ASN103 5.0 30.8 1.0

Calcium binding site 6 out of 10 in 5ele

Go back to Calcium Binding Sites List in 5ele
Calcium binding site 6 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca204

b:15.2
occ:1.00
 O4 C:BCN201 2.2 22.7 1.0
OE2 C:GLU79 2.3 21.6 1.0
O C:HOH361 2.4 27.4 1.0
O6 C:BCN201 2.4 21.5 1.0
O21 C:BCN201 2.4 18.9 1.0
OE1 I:GLU79 2.5 18.9 1.0
OE2 I:GLU79 2.6 17.8 1.0
N1 C:BCN201 2.7 21.8 1.0
CD I:GLU79 2.9 18.8 1.0
C4 C:BCN201 3.3 23.1 1.0
C2 C:BCN201 3.3 21.8 1.0
C6 C:BCN201 3.4 20.5 1.0
CD C:GLU79 3.5 20.6 1.0
C5 C:BCN201 3.5 21.1 1.0
C1 C:BCN201 3.5 22.6 1.0
C3 C:BCN201 3.5 21.7 1.0
CA C:CA202 4.0 15.5 1.0
O C:HOH301 4.0 24.6 1.0
CG C:GLU79 4.1 18.8 1.0
O I:HOH360 4.3 37.4 1.0
CG I:GLU79 4.4 17.0 1.0
O C:HOH302 4.4 35.1 1.0
OE1 C:GLU79 4.5 20.4 1.0
ND2 B:ASN103 4.5 36.1 1.0
O22 C:BCN201 4.5 20.2 1.0
O4 C:BCN203 4.6 25.4 1.0
NZ I:LYS23 4.7 21.2 0.5
CB B:ASN103 5.0 36.5 1.0

Calcium binding site 7 out of 10 in 5ele

Go back to Calcium Binding Sites List in 5ele
Calcium binding site 7 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:14.2
occ:1.00
 O4 D:BCN203 2.3 24.2 1.0
OE2 H:GLU79 2.3 16.9 1.0
O6 D:BCN203 2.4 19.7 1.0
O22 D:BCN203 2.4 18.1 1.0
O G:HOH333 2.4 28.0 1.0
OE1 D:GLU79 2.5 17.6 1.0
OE2 D:GLU79 2.5 17.3 1.0
N1 D:BCN203 2.8 22.0 1.0
CD D:GLU79 2.8 16.4 1.0
C2 D:BCN203 3.3 19.6 1.0
C4 D:BCN203 3.3 24.2 1.0
C6 D:BCN203 3.4 21.2 1.0
C5 D:BCN203 3.5 22.2 1.0
CD H:GLU79 3.5 16.2 1.0
C3 D:BCN203 3.5 22.2 1.0
C1 D:BCN203 3.5 21.0 1.0
CA D:CA204 4.0 14.6 1.0
O D:HOH352 4.2 23.6 1.0
O D:HOH303 4.2 39.9 1.0
CG H:GLU79 4.2 15.2 1.0
O D:HOH309 4.2 37.4 1.0
CG D:GLU79 4.3 14.9 1.0
O H:HOH303 4.4 33.1 1.0
O21 D:BCN203 4.5 17.7 1.0
OE1 H:GLU79 4.5 17.6 1.0
O6 D:BCN201 4.5 26.9 1.0
OXT G:ASN103 4.8 55.7 1.0
OD1 G:ASN103 4.9 47.7 1.0
CB G:ASN103 5.0 46.7 1.0

Calcium binding site 8 out of 10 in 5ele

Go back to Calcium Binding Sites List in 5ele
Calcium binding site 8 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca204

b:14.6
occ:1.00
 O6 D:BCN201 2.2 26.9 1.0
O21 D:BCN201 2.3 15.8 1.0
OE2 D:GLU79 2.3 17.3 1.0
OE1 H:GLU79 2.4 17.6 1.0
O4 D:BCN201 2.4 26.6 1.0
O D:HOH352 2.5 23.6 1.0
OE2 H:GLU79 2.5 16.9 1.0
CD H:GLU79 2.8 16.2 1.0
N1 D:BCN201 3.1 24.5 1.0
C6 D:BCN201 3.2 28.5 1.0
C2 D:BCN201 3.2 21.3 1.0
C3 D:BCN201 3.2 25.4 1.0
C4 D:BCN201 3.3 25.8 1.0
C1 D:BCN201 3.5 22.9 1.0
C5 D:BCN201 3.5 25.6 1.0
CD D:GLU79 3.5 16.4 1.0
CA D:CA202 4.0 14.2 1.0
O G:HOH333 4.1 28.0 1.0
O H:HOH321 4.1 40.3 1.0
CG D:GLU79 4.2 14.9 1.0
O D:HOH303 4.2 39.9 1.0
ND2 C:ASN103 4.3 49.3 1.0
CG H:GLU79 4.3 15.2 1.0
O22 D:BCN201 4.4 18.4 1.0
O D:HOH311 4.5 32.9 1.0
OE1 D:GLU79 4.6 17.6 1.0
O4 D:BCN203 4.6 24.2 1.0
CB C:ASN103 4.7 43.1 1.0
O D:HOH380 4.9 51.1 1.0

Calcium binding site 9 out of 10 in 5ele

Go back to Calcium Binding Sites List in 5ele
Calcium binding site 9 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca202

b:13.4
occ:1.00
 O4 E:BCN203 2.2 29.2 1.0
OE2 G:GLU79 2.3 16.5 1.0
O21 E:BCN203 2.4 17.7 1.0
O6 E:BCN203 2.4 22.2 1.0
OE1 E:GLU79 2.4 16.6 1.0
O F:HOH332 2.4 27.9 1.0
OE2 E:GLU79 2.5 15.8 1.0
N1 E:BCN203 2.7 22.9 1.0
CD E:GLU79 2.8 16.7 1.0
C4 E:BCN203 3.2 29.0 1.0
C2 E:BCN203 3.3 19.9 1.0
C6 E:BCN203 3.4 21.8 1.0
C5 E:BCN203 3.4 22.9 1.0
C3 E:BCN203 3.5 24.6 1.0
CD G:GLU79 3.5 16.5 1.0
C1 E:BCN203 3.6 21.8 1.0
CA E:CA204 3.9 14.5 1.0
O E:HOH363 4.0 27.6 1.0
CG G:GLU79 4.2 14.3 1.0
O6 E:BCN201 4.3 27.3 1.0
CG E:GLU79 4.3 15.3 1.0
OE1 G:GLU79 4.4 18.8 1.0
O22 E:BCN203 4.5 17.1 1.0
O E:HOH303 4.5 29.9 1.0
OD1 F:ASN103 4.6 42.0 1.0
OXT F:ASN103 4.8 36.0 1.0

Calcium binding site 10 out of 10 in 5ele

Go back to Calcium Binding Sites List in 5ele
Calcium binding site 10 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Cholera Toxin El Tor B-Pentamer in Complex with A Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca204

b:14.5
occ:1.00
 O6 E:BCN201 1.9 27.3 1.0
OE2 E:GLU79 2.3 15.8 1.0
O22 E:BCN201 2.3 19.4 1.0
O E:HOH363 2.4 27.6 1.0
O4 E:BCN201 2.4 20.8 1.0
OE1 G:GLU79 2.5 18.8 1.0
OE2 G:GLU79 2.6 16.5 1.0
CD G:GLU79 2.9 16.5 1.0
C6 E:BCN201 3.1 27.9 1.0
N1 E:BCN201 3.1 23.8 1.0
C2 E:BCN201 3.3 20.8 1.0
C5 E:BCN201 3.4 24.9 1.0
C4 E:BCN201 3.4 23.1 1.0
C3 E:BCN201 3.5 23.9 1.0
CD E:GLU79 3.5 16.7 1.0
C1 E:BCN201 3.5 23.9 1.0
CA E:CA202 3.9 13.4 1.0
O F:HOH332 4.0 27.9 1.0
O G:HOH373 4.2 36.3 1.0
CG E:GLU79 4.2 15.3 1.0
O4 E:BCN203 4.3 29.2 1.0
CG G:GLU79 4.4 14.3 1.0
OE1 E:GLU79 4.4 16.6 1.0
O21 E:BCN201 4.5 20.0 1.0
O D:HOH344 4.5 36.3 1.0
ND2 D:ASN103 4.7 47.8 1.0

Reference:

J.E.Heggelund, D.Burschowsky, V.A.Bjrnestad, V.Hodnik, G.Anderluh, U.Krengel. High-Resolution Crystal Structures Elucidate the Molecular Basis of Cholera Blood Group Dependence. Plos Pathog. V. 12 05567 2016.
ISSN: ESSN 1553-7374
PubMed: 27082955
DOI: 10.1371/JOURNAL.PPAT.1005567
Page generated: Sun Jul 14 18:40:11 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy